Background In this study, we wanted to assess the menstrual awareness among urban and rural adolescent girls and compare the menstrual hygiene practices among them. Methods This was a hospital based cross-sectional study conducted among 170 adolescent girls attending the OPD of Gynaecology, Paediatrics and General Medicine at Government Medical College, Thrissur District, Kerala. It was carried for a period of one year after obtaining clearance from the institutional ethics committee and written informed consent from the study participants. They were provided with a validated questionnaire to assess menstrual awareness hygiene practice among them. Results Majority (89.4%) from the urban area of residence believed that it was physiological, while majority (54.1%) from the rural areas didn’t know the actual cause for menstruation. This difference between the rural and urban areas on awareness about the cause of menstruation was found to be statistically significant. More than half of the subjects used sanitary pads during menstruation. The frequency of changing pads at school was less in both urban and rural groups. The reusage of pads was almost similar among rural and urban study subjects with around 23.5% and 22.4% of them reusing the pads respectively in both the groups. Awareness regarding menstrual cup was more in urban group compared to rural. But restrictions during menstruation was practised more in rural group that is 70% compared to urban group which was roughly 52%. Conclusion Menstrual health forms the most important stepping stone to women’s sexual and reproductive health. One third of the study population was not at all aware of the cause of menstruation. There was significant difference in various menstrual hygiene practices among urban and rural girls. Many restrictions were practiced during menstruation more in rural group. A concerted effort from parents, educational institutions and existing healthcare institutions along with media may ensure safe and secure reproductive health prospects for adolescents in the region.